# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:15:01 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N-{3-[(3-aminopropyl)amino]propyl}butane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCNCCCNCCCN
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 TER  TER  N-{3-[(3-aminopropyl)amino]propyl}butane-1,4-diamine  ligand  40  14  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TER
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 TER  N1    N  NH2   0  -0.800   0.4826   0.0613  -7.9624
 TER  C2    C  CH2   0  -0.273  -0.3999   0.0559  -6.8035
 TER  C3    C  CH2   0  -0.453   0.4012  -0.0006  -5.5119
 TER  C4    C  CH2   0  -0.253  -0.4890  -0.0023  -4.2790
 TER  N5    N  NH1   0  -0.599   0.2923  -0.0675  -3.0587
 TER  C6    C  CH2   0  -0.250  -0.5274  -0.0384  -1.8625
 TER  C7    C  CH2   0  -0.469   0.3247  -0.0890  -0.6041
 TER  C8    C  CH2   0  -0.250  -0.5168  -0.0533   0.6620
 TER  N9    N  NH1   0  -0.601   0.3129  -0.1050   1.8504
 TER  C10   C  CH2   0  -0.246  -0.4535  -0.0334   3.0796
 TER  C11   C  CH2   0  -0.446   0.4499  -0.0594   4.3026
 TER  C12   C  CH2   0  -0.429  -0.3291   0.0274   5.6080
 TER  C13   C  CH2   0  -0.271   0.5741  -0.0020   6.8316
 TER  N14   N  NH2   0  -0.801  -0.2056   0.0909   8.0582
 TER  HN11  H  HNH2  0   0.337   0.9950   0.9349  -7.9825
 TER  HN12  H  HNH2  0   0.345  -0.0730   0.0552  -8.8082
 TER  H21   H  HCH2  0   0.213  -1.0392  -0.8294  -6.8650
 TER  H22   H  HCH2  0   0.189  -1.0775   0.9215  -6.7669
 TER  H31   H  HCH2  0   0.214   1.0773   0.8615  -5.4686
 TER  H32   H  HCH2  0   0.219   1.0301  -0.8952  -5.5116
 TER  H41   H  HCH2  0   0.212  -1.1470  -0.8774  -4.3108
 TER  H42   H  HCH2  0   0.183  -1.1528   0.8781  -4.3062
 TER  HN5   H  HNH1  0   0.334   0.9241   0.7256  -3.0367
 TER  H61   H  HCH2  0   0.213  -1.1929  -0.9080  -1.8832
 TER  H62   H  HCH2  0   0.184  -1.1842   0.8467  -1.8245
 TER  H71   H  HCH2  0   0.217   1.0163   0.7617  -0.6016
 TER  H72   H  HCH2  0   0.222   0.9372  -0.9947  -0.6122
 TER  H81   H  HCH2  0   0.213  -1.1879  -0.9188   0.6748
 TER  H82   H  HCH2  0   0.184  -1.1683   0.8365   0.6429
 TER  HN9   H  HNH1  0   0.334   0.9583   0.6771   1.8271
 TER  H101  H  HCH2  0   0.212  -1.1303  -0.8939   3.1130
 TER  H102  H  HCH2  0   0.182  -1.0974   0.8615   3.1228
 TER  H111  H  HCH2  0   0.213   1.1578   0.7753   4.2452
 TER  H112  H  HCH2  0   0.216   1.0494  -0.9754   4.2868
 TER  H121  H  HCH2  0   0.214  -1.0444  -0.7989   5.6718
 TER  H122  H  HCH2  0   0.212  -0.9203   0.9504   5.6188
 TER  H131  H  HCH2  0   0.187   1.3304   0.7904   6.7318
 TER  H132  H  HCH2  0   0.211   1.1234  -0.9477   6.8455
 TER  HN41  H  HNH2  0   0.345   0.4132   0.0366   8.8571
 TER  HN42  H  HNH2  0   0.336  -0.6330   1.0079   8.1094

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 TER  N1   C2    single  1.457  0.020  1.457
 TER  N1   HN11  single  0.890  0.020  1.040
 TER  N1   HN12  single  0.890  0.020  1.040
 TER  C2   C3    single  1.521  0.020  1.521
 TER  C2   H21   single  0.970  0.020  1.090
 TER  C2   H22   single  0.970  0.020  1.090
 TER  C3   C4    single  1.521  0.020  1.521
 TER  C3   H31   single  0.970  0.020  1.090
 TER  C3   H32   single  0.970  0.020  1.090
 TER  C4   N5    single  1.450  0.020  1.450
 TER  C4   H41   single  0.970  0.020  1.090
 TER  C4   H42   single  0.970  0.020  1.090
 TER  N5   C6    single  1.450  0.020  1.450
 TER  N5   HN5   single  0.890  0.020  1.040
 TER  C6   C7    single  1.521  0.020  1.521
 TER  C6   H61   single  0.970  0.020  1.090
 TER  C6   H62   single  0.970  0.020  1.090
 TER  C7   C8    single  1.521  0.020  1.521
 TER  C7   H71   single  0.970  0.020  1.090
 TER  C7   H72   single  0.970  0.020  1.090
 TER  C8   N9    single  1.450  0.020  1.450
 TER  C8   H81   single  0.970  0.020  1.090
 TER  C8   H82   single  0.970  0.020  1.090
 TER  N9   C10   single  1.450  0.020  1.450
 TER  N9   HN9   single  0.890  0.020  1.040
 TER  C10  C11   single  1.521  0.020  1.521
 TER  C10  H101  single  0.970  0.020  1.090
 TER  C10  H102  single  0.970  0.020  1.090
 TER  C11  C12   single  1.523  0.020  1.523
 TER  C11  H111  single  0.970  0.020  1.090
 TER  C11  H112  single  0.970  0.020  1.090
 TER  C12  C13   single  1.521  0.020  1.521
 TER  C12  H121  single  0.970  0.020  1.090
 TER  C12  H122  single  0.970  0.020  1.090
 TER  C13  N14   single  1.456  0.020  1.456
 TER  C13  H131  single  0.970  0.020  1.090
 TER  C13  H132  single  0.970  0.020  1.090
 TER  N14  HN41  single  0.890  0.020  1.040
 TER  N14  HN42  single  0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 TER  HN12  N1   HN11  105.44  3.000
 TER  HN12  N1   C2    109.40  3.000
 TER  HN11  N1   C2    108.99  3.000
 TER  H22   C2   H21   106.19  3.000
 TER  H22   C2   C3    108.99  3.000
 TER  H21   C2   C3    109.00  3.000
 TER  H22   C2   N1    113.38  3.000
 TER  H21   C2   N1    108.21  3.000
 TER  C3    C2   N1    110.89  3.000
 TER  H32   C3   H31   106.77  3.000
 TER  H32   C3   C4    109.61  3.000
 TER  H31   C3   C4    109.26  3.000
 TER  H32   C3   C2    109.49  3.000
 TER  H31   C3   C2    109.22  3.000
 TER  C4    C3   C2    112.35  3.000
 TER  H42   C4   H41   105.99  3.000
 TER  H42   C4   N5    112.38  3.000
 TER  H41   C4   N5    108.18  3.000
 TER  H42   C4   C3    109.36  3.000
 TER  H41   C4   C3    109.21  3.000
 TER  N5    C4   C3    111.52  3.000
 TER  HN5   N5   C6    108.57  3.000
 TER  HN5   N5   C4    108.58  3.000
 TER  C6    N5   C4    112.86  3.000
 TER  H62   C6   H61   106.02  3.000
 TER  H62   C6   C7    109.38  3.000
 TER  H61   C6   C7    109.25  3.000
 TER  H62   C6   N5    112.41  3.000
 TER  H61   C6   N5    108.18  3.000
 TER  C7    C6   N5    111.42  3.000
 TER  H72   C7   H71   106.82  3.000
 TER  H72   C7   C8    109.61  3.000
 TER  H71   C7   C8    109.21  3.000
 TER  H72   C7   C6    109.59  3.000
 TER  H71   C7   C6    109.24  3.000
 TER  C8    C7   C6    112.22  3.000
 TER  H82   C8   H81   106.02  3.000
 TER  H82   C8   N9    112.39  3.000
 TER  H81   C8   N9    108.22  3.000
 TER  H82   C8   C7    109.35  3.000
 TER  H81   C8   C7    109.28  3.000
 TER  N9    C8   C7    111.39  3.000
 TER  HN9   N9   C10   108.52  3.000
 TER  HN9   N9   C8    108.52  3.000
 TER  C10   N9   C8    112.98  3.000
 TER  H102  C10  H101  105.99  3.000
 TER  H102  C10  C11   109.21  3.000
 TER  H101  C10  C11   109.22  3.000
 TER  H102  C10  N9    112.43  3.000
 TER  H101  C10  N9    108.28  3.000
 TER  C11   C10  N9    111.52  3.000
 TER  H112  C11  H111  106.42  3.000
 TER  H112  C11  C12   109.89  3.000
 TER  H111  C11  C12   109.39  3.000
 TER  H112  C11  C10   109.15  3.000
 TER  H111  C11  C10   109.19  3.000
 TER  C12   C11  C10   112.62  3.000
 TER  H122  C12  H121  106.41  3.000
 TER  H122  C12  C13   109.18  3.000
 TER  H121  C12  C13   109.05  3.000
 TER  H122  C12  C11   109.42  3.000
 TER  H121  C12  C11   109.95  3.000
 TER  C13   C12  C11   112.63  3.000
 TER  H132  C13  H131  106.18  3.000
 TER  H132  C13  N14   108.26  3.000
 TER  H131  C13  N14   113.49  3.000
 TER  H132  C13  C12   108.97  3.000
 TER  H131  C13  C12   108.75  3.000
 TER  N14   C13  C12   111.00  3.000
 TER  HN42  N14  HN41  105.46  3.000
 TER  HN42  N14  C13   109.04  3.000
 TER  HN41  N14  C13   109.52  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 TER  Var_01  C4    C3   C2   N1    179.78  30.0  3
 TER  Var_02  N5    C4   C3   C2    179.53  30.0  3
 TER  Var_03  C6    N5   C4   C3    178.61  30.0  3
 TER  Var_04  C7    C6   N5   C4   -179.22  30.0  3
 TER  Var_05  C8    C7   C6   N5    179.75  30.0  3
 TER  Var_06  N9    C8   C7   C6    179.89  30.0  3
 TER  Var_07  C10   N9   C8   C7    178.30  30.0  3
 TER  Var_08  C11   C10  N9   C8   -178.75  30.0  3
 TER  Var_09  C12   C11  C10  N9    179.48  30.0  3
 TER  Var_10  C13   C12  C11  C10   179.86  30.0  3
 TER  Var_11  N14   C13  C12  C11   179.66  30.0  3
 TER  Var_12  HN11  N1   C2   C3    -67.82  30.0  3
 TER  Var_13  HN41  N14  C13  C12   178.03  30.0  3

